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- PDB-1aus: ACTIVATED UNLIGANDED SPINACH RUBISCO -

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Basic information

Entry
Database: PDB / ID: 1aus
TitleACTIVATED UNLIGANDED SPINACH RUBISCO
Components(RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE) x 2
KeywordsLYASE (CARBON-CARBON)
Function / homology
Function and homology information


photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / chloroplast / monooxygenase activity / magnesium ion binding
Similarity search - Function
Ribulose-1,5-bisphosphate carboxylase small subunit, N-terminal / Ribulose-1,5-bisphosphate carboxylase small subunit / Ribulose bisphosphate carboxylase, small subunit / Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase / Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain ...Ribulose-1,5-bisphosphate carboxylase small subunit, N-terminal / Ribulose-1,5-bisphosphate carboxylase small subunit / Ribulose bisphosphate carboxylase, small subunit / Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase / Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase large subunit, type I / Ribulose bisphosphate carboxylase, large chain, active site / Ribulose bisphosphate carboxylase large chain active site. / Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal / Ribulose bisphosphate carboxylase large chain, N-terminal domain / Ribulose bisphosphate carboxylase, large subunit, C-terminal / RuBisCO / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain superfamily / RuBisCO large subunit, N-terminal domain superfamily / Ribulose bisphosphate carboxylase large chain, catalytic domain / Alpha-Beta Plaits / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Ribulose bisphosphate carboxylase large chain / Ribulose bisphosphate carboxylase small subunit, chloroplastic 2
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsTaylor, T.C. / Andersson, I.
Citation
Journal: Biochemistry / Year: 1997
Title: Structure of a product complex of spinach ribulose-1,5-bisphosphate carboxylase/oxygenase.
Authors: Taylor, T.C. / Andersson, I.
#1: Journal: J.Mol.Biol. / Year: 1990
Title: Crystallographic Analysis of Ribulose 1,5-Bisphosphate Carboxylase from Spinach at 2.4 Angstroms Resolution
Authors: Knight, S. / Andersson, I. / Branden, C.-I.
#2: Journal: Science / Year: 1989
Title: Reexamination of the Three-Dimensional Structure of the Small Subunit of Ru(Dot)Bis(Dot)Co from Higher Plants
Authors: Knight, S. / Andersson, I. / Branden, C.-I.
#3: Journal: Nature / Year: 1989
Title: Crystal Structure of the Active Site of Ribulose-Bisphosphate Carboxylase
Authors: Andersson, I. / Knight, S. / Schneider, G. / Lindqvist, Y. / Lundqvist, T. / Branden, C.-I. / Lorimer, G.H.
History
DepositionJun 21, 1995Processing site: BNL
Revision 1.0Oct 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
S: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
M: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
T: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
N: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
U: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
O: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
V: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)269,77516
Polymers269,4938
Non-polymers2818
Water4,342241
1
L: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
S: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
M: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
T: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
N: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
U: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
O: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
V: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
hetero molecules

L: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
S: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
M: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
T: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
N: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
U: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
O: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
V: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)539,54932
Polymers538,98716
Non-polymers56316
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area96330 Å2
ΔGint-401 kcal/mol
Surface area118030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.400, 158.700, 203.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Atom site foot note1: CIS PROLINE - PRO L 176
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.000952, 0.999993, 0.003663), (-0.999996, 0.000962, -0.00262), (-0.002624, -0.00366, 0.99999)-37.715, 37.5602, 0.0937
2given(-0.999987, -0.000966, 0.005092), (0.000965, -1, -0.000101), (0.005092, -9.6E-5, 0.999987)-0.2391, 75.1369, 0.0132
3given(0.000191, -0.999997, 0.002594), (1, 0.00019, -0.000272), (0.000272, 0.002594, 0.999997)37.4187, 37.6305, -0.1041
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 L 20 .. L 463 ? 20 .. ? 463 M1 S 1 .. S 123 ? 1 .. ? 123 M2 L 20 .. L 463 ? 20 .. ? 463 M2 S 1 .. S 123 ? 1 .. ? 123 M3 L 20 .. L 463 ? 20 .. ? 463 M3 S 1 .. S 123 ? 1 .. ? 123 THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CONTAINS FOUR LARGE AND FOUR SMALL SUBUNITS RELATED BY A FOUR-FOLD AXIS THROUGH THE MOLECULAR CENTER AT X=0, Y=1/4, Z=1/4. THE TRANSFORMATIONS GIVEN IN THE *MTRIX* RECORDS BELOW WILL GENERATE AN L4S4 HALF-MOLECULE FROM THE COORDINATES IN ENTRY. TO GENERATE THE FULL L8S8 MOLECULE FROM L4S4 THE FOLLOWING TWO-FOLD ROTATION ABOUT THE CRYSTALLOGRAPHIC TWO-FOLD AXIS ALONG Y HAS TO BE APPLIED: SYMMETRY1 1 -1.000000 0.000000 0.000000 0.00000 SYMMETRY2 1 0.000000 1.000000 0.000000 0.00000 SYMMETRY3 1 0.000000 0.000000 -1.000000 101.50000

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Components

#1: Protein
RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE / RUBISCO


Mass: 52734.680 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / Organ: LEAF
References: UniProt: P00875, ribulose-bisphosphate carboxylase
#2: Protein
RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE / RUBISCO


Mass: 14638.671 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / Organ: LEAF
References: UniProt: Q43832, ribulose-bisphosphate carboxylase
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O
Compound detailsRESIDUE L 201 IS A MODIFIED ACTIVATOR LYSINE WHICH IS CARBAMYLATED AT THE EPSILON-AMINO GROUP. THE ...RESIDUE L 201 IS A MODIFIED ACTIVATOR LYSINE WHICH IS CARBAMYLATED AT THE EPSILON-AMINO GROUP. THE CARBAMYL ACTIVATOR GROUP IS PRESENTED AS HET GROUP *CBX* AT THE END OF CHAIN *L*.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.68 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: Taylor, T.C., (1996) Nat. Struct. Biol., 3, 95.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150-60 mg/mlprotein1drop
2100 mM3-PGA1drop
314-16 %PEG40001reservoir
40.2 M1reservoirNaCl
525 mMHEPES1reservoir
610 mM1reservoirMgCl2
750 mM1reservoirNaHCO3
80.02 %1reservoirNaN3

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 28, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 130977 / % possible obs: 89 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Rmerge(I) obs: 0.105
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 20 Å / Num. obs: 107965 / % possible obs: 85 % / Num. measured all: 799161 / Rmerge(I) obs: 0.103

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.2→7 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.239 -5 %
Rwork0.217 --
obs0.217 117630 94.8 %
Displacement parametersBiso mean: 16.01 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 2.2→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17892 0 16 241 18149
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.207 / Rfactor Rfree: 0.224 / Rfactor Rwork: 0.207
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 16.019 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.667

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